@misc{Szadkowska_Paulina_Róża_Application_2023,
 author={Szadkowska, Paulina Róża},
 editor={Kamińska-Kaczmarek, Bożena (1961– ) : Supervisor},
 address={Warsaw},
 howpublished={online},
 year={2023},
 school={Instytut Biologii Doświadczalnej im. Marcelego Nenckiego PAN},
 publisher={Instytut Biologii Doświadczalnej im. Marcelego Nenckiego PAN},
 language={eng},
 abstract={Gliomas are primary tumors of the central nervous system. Diagnosis and therapy recommendations are difficult, because of the intertumoral heterogenicity of glial tumors. Current World Health Organization classification of gliomas is based on the pathomorphological and molecular characteristics of the tumor biopsy. Diagnosis is based on pathomorphological features (diffusiveness, proliferation index, a presence of necrosis) and upon specific genetic alterations detected in the tumor, which leads to specific recommendations for the therapy. Next generation sequencing (NGS) is a valuable tool to improve diagnostics of brain tumors. Traditional tissue biopsy might not present complete mutational spectrum in case of such heterogenic tumors, so alternative methods are being tested to enable more holistic view of each disease. When traditional biopsy or tumor resection are not possible, a liquid biopsy would be of great assistance to clinical practice. Liquid biopsy is a use of bodily fluids to isolate circulating cell free nucleic acids or circulating tumor cells to detect cancer markers for diagnostics, disease monitoring or prognostic. In case of primary brain tumors, cerebrospinal fluid can contain more circulating cell free DNA (cfDNA) or RNA (cfRNA) originating from the tumor, but a lumbar puncture may have side effects, so it is rarely performed on heavily symptomatic primary brain tumor patients. We sought to evaluate if improvements in cfDNA isolation, library preparation and targeted sequencing would provide reliable information regards genetic alterations in glioblastoma (GBM), most common and deadly primary brain tumor. After analysis of blood derived cfDNA potentially pathogenic variants were detected in 37/84, which based upon the current literature is an improvement from most of the studies. We employed a target gene panel encompassing 668 cancer-related genes and NGS to a set of diagnostically difficult pediatric glioma tumors. The analysis of DNA isolated from formalin fixed paraffin embedded (FFPE) sections originating from those tumors yielded the whole spectrum of potentially pathogenic mutations, some interesting variants were found, that could be further studied (MTUS, FANCA, RET). Tumor-derived cell cultures are valuable in vitro system to study tumorigenesis and screen for therapeutics, however it is not fully known if tumor cells keep their genetic alterations and cultured clones reflect molecular profile of an original tumor. Comparative analysis of somatic mutations present in tumor-derived cell lines and/or original tumors have shown some differences in variant profiles, cell cultures contained more detectable somatic mutations. This can indicate that some somatic variants can be missed in the tissue biopsy, due to its complexity as tumor contains healthy cells, microglia and macrophages that can make background noise decreasing the tumor variants detectability. On the other hand, tumor stem cells can possibly gain mutations during cell culture, as their DNA repair pathways are frequently malfunctioning, and mitosis is maximized by artificial growth factors. The current classification of gliomas is based upon tumor genotyping. Current diagnostic tests employ molecular analysis of DNA isolated from FFPE or frozen tumor samples. There are many ongoing clinical and research studies improving current diagnostic methods with the aim to create personalized therapy recommendations with use of both blood derived cfDNA and tumor derived cell cultures. Present study demonstrates how tumor derived cell lines and blood derived cfDNA can offer an insight on tumor genetic heterogeneity.},
 title={Application of targeted next-generation sequencing to detect potentially pathogenic alterations in gliomas, circulating tumor DNA and tumor-derived cells : PhD thesis},
 type={Text},
 URL={http://rcin.org.pl/Content/240090/WA488_276491_20281_Szadkowska-Paulina-2023.pdf},
 keywords={DNA, Glioma - Diagnosis, Nucleic acid sequencing, Tumor cells},
}